Large-scale cDNA sequencing efforts conducted by our lab and others have provided strong evidence that, in sharp contrast to earlier understanding, much of the human genome is transcribed into non-protein-coding RNA (ncRNA). Human ncRNA transcription is extremely widespread and pervasive with potentially broad implications for neuronal function. Both short ncRNA, such as microRNA (miRNA) and long ncRNA, like natural antisense transcripts (NATs) are reported as modulators of transcription by induction of DNA methylation and chromatin remodeling. This application focuses on the role of ncRNA as epigenomic modulators of Alzheimer's disease. Our recent publication (Nature Medicine 10.1038/nm.1784,July 2008) demonstrates that ncRNA exert a pivotal role in Alzheimer's disease pathophysiology. The reports on the role of various families of ncRNA in neurological disorders highlight the fact that ncRNA-mediated epigenomic modulation of transcription is pervasive and appear particularly prominent in the nervous system. Several functions proposed for ncRNA, among them regulation of chromatin architecture and epigenetic memory, have received much attention. Importantly, modifications of chromatin structure induced by ncRNA are suggested as many histone methyl transferase (HMTase) complexes lack DNA-binding domains but possess RNA- binding motifs. Both trimethylated K4 on H3 (a mark of active transcription) and trimethylated K27 on H3 (a mark of repressed chromatin) were reported in association with ncRNAs, suggesting a scaffold model for the ncRNA in guiding chromatin modification. Here, we describe an approach to create a comprehensive epigenomic inventory of long and short ncRNA associated with Alzheimer's disease. We shall include both long and short ncRNAs by employing a NAT-specific siRNA library as well as a deep sequencing approach to create a catalog of ncRNA's involved in the pathogenesis of Alzheimer's disease. By applying Chromatin immunoprecipitation (ChIP), as well as MS2 RNA tagging and Cryogenic- immunoprecipitation, (Cryo-IP) followed by deep sequencing of RNA fractions (ChIP-Seq) and Mass-spectrometry of protein fractions, we will study RNA-chromatin, RNA-RNA and RNA- protein interactions. Further, we will validate involvement of candidate epigenomic modulators of Alzheimer's disease by studying different sets of human brain RNA derived from Alzheimer's disease patients and control individuals. The experiments proposed in this application promise to yield significant insights into epigenomic mechanisms by which gene expression is controlled. Furthermore we postulate that ncRNAs will prove to be broadly involved in the pathogenesis of Alzheimer's disease. Importantly, detailed studies on Alzheimer's disease-related ncRNAs will potentially lead to the discovery of novel therapeutic targets and/or biomarkers. PUBLIC HEALTH RELEVANCE: Alzheimer's disease is a devastating age-related neurodegenerative disorder characterized by progressive impairment of cognition and short-term memory loss. Despite considerable research efforts, researchers are still a long way from the ultimate goal of revealing clear risk factors that can help in the diagnosis, prevention and treatment of the disease. Current theories about the development of common late-onset Alzheimer's disease hinge on the premise that Alzheimer's disease arises mainly from heritable causes. However, these genetic causes are at least in part atypical (nonconventional), and we therefore argue that so-called "epigenetic/epigenomic" causes must be considered.